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BACKGROUND & CHANGES

This update mirrors behavior in broadinstitute/scp-ingest-pipeline#402 to use OLS as a fallback validation for taxon IDs that do not appear in the "slim" minified version we use for both client- and server-side validation. This allows for a greater breadth of values while still maintaining quick validation in most cases.

MANUAL TESTING

  1. Boot as normal and create a new AnnData study
  2. Upload the file at test/test_data/anndata/valid_extended_taxon.h5ad and confirm no errors are found

@bistline bistline requested a review from eweitz November 26, 2025 21:33
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codecov bot commented Nov 26, 2025

Codecov Report

❌ Patch coverage is 95.55556% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.53%. Comparing base (194c2ea) to head (b9a0922).
⚠️ Report is 27 commits behind head on development.

Files with missing lines Patch % Lines
...p/javascript/lib/validation/ontology-validation.js 93.75% 1 Missing ⚠️
app/javascript/lib/validation/validate-anndata.js 0.00% 1 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@               Coverage Diff               @@
##           development    #2329      +/-   ##
===============================================
- Coverage        72.58%   72.53%   -0.06%     
===============================================
  Files              335      335              
  Lines            27834    27919      +85     
  Branches          2565     2587      +22     
===============================================
+ Hits             20204    20251      +47     
- Misses            7486     7524      +38     
  Partials           144      144              
Files with missing lines Coverage Δ
app/javascript/lib/validation/shared-validation.js 97.79% <100.00%> (+0.37%) ⬆️
...javascript/lib/validation/validate-file-content.js 89.13% <100.00%> (+0.04%) ⬆️
...p/javascript/lib/validation/ontology-validation.js 96.77% <93.75%> (-0.67%) ⬇️
app/javascript/lib/validation/validate-anndata.js 84.67% <0.00%> (ø)

... and 5 files with indirect coverage changes

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@bistline bistline merged commit 509b2c5 into development Dec 1, 2025
6 checks passed
@github-actions github-actions bot deleted the jb-ols-taxon-fallback branch December 1, 2025 21:28
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3 participants